Vibrio bivalvicida is a novel pathogen of bivalve larvae responsible for recent vibriosis outbreaks affecting shellfish hatcheries. Here, we announce the draft genome sequence of V. bivalvicida 605 and describe potential virulence factors

Barja, Juan L

Dubert, Javier

Gomez-Chiarri, Marta

Nelson, David R.

Romalde, Jesus L

Spinard, Edward J

English

PubMed

DigitalCommons@URI

University of Rhode IslandDigitalCommons@URICell and Molecular Biology Faculty Publications Cell and Molecular Biology2016Draft Genome Sequence of the New Pathogen forBivalve Larvae Vibrio bivalvicidaJavier DubertEdward J. SpinardUniversity of Rhode IslandSee next page for additional authorsCreative Commons LicenseCreative Commons LicenseThis work is licensed under a Creative Commons Attribution 4.0 License.Follow this and additional works at: https://digitalcommons.uri.edu/cmb_facpubsThis Article is brought to you for free and open access by the Cell and Molecular Biology at DigitalCommons@URI. It has been accepted for inclusionin Cell and Molecular Biology Faculty Publications by an authorized administrator of DigitalCommons@URI. For more information, please contactdigitalcommons@etal.uri.edu.Citation/Publisher AttributionDubert, J., Spinard, E. J., Nelson, D. R., Gomez-Chiarri, M., Romalde, J. L., and Barja, J. L. (2016). Draft genome sequence of the newpathogen for bivalve larvae Vibrio bivalvicida. Genome Announcements, 4(2), e00216-16. doi:10.1128/genomeA.00216-16Available at: http://dx.doi.org/10.1128/genomeA.00216-16AuthorsJavier Dubert, Edward J. Spinard, David R. Nelson, Marta Gomez-Chiarri, Jesus L. Romalde, and Juan L. BarjaThis article is available at DigitalCommons@URI: https://digitalcommons.uri.edu/cmb_facpubs/32Draft Genome Sequence of the New Pathogen for Bivalve LarvaeVibrio bivalvicidaJavier Dubert,a Edward J. Spinard,b David R. Nelson,b Marta Gomez-Chiarri,c Jesús L. Romalde,a Juan L. BarjaaDepartamento de Microbiología y Parasitología, CIBUS–Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spaina; Department ofCell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USAb; Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island.Kingston, Rhode Island, USAcVibrio bivalvicida is a novel pathogen of bivalve larvae responsible for recent vibriosis outbreaks affecting shellfish hatcheries.Here, we announce the draft genome sequence of V. bivalvicida 605T and describe potential virulence factors.Received 17 February 2016 Accepted 24 February 2016 Published 7 April 2016Citation Dubert J, Spinard EJ, Nelson DR, Gomez-Chiarri M, Romalde JL, Barja JL. 2016. Draft genome sequence of the new pathogen for bivalve larvae Vibrio bivalvicida.Genome Announc 4(2):e00216-16. doi:10.1128/genomeA.00216-16.Copyright © 2016 Dubert et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Juan L. Barja, juanluis.barja@usc.es.The genus Vibrio is the largest member of the family Vibrion-aceae and comprises more than 126 bacterial species and 2subspecies (http://www.bacterio.net/vibrio.html) clustered in 18clades and 4 orphan species (1, 2). Vibrios are widespread in ma-rine environments, showing high diversity at the metabolic andecological levels, and their association with marine bivalves hasregularly been reported (3). Vibriosis caused by some Vibrio spp.represents the main bottleneck of the production process at bi-valve hatcheries due to the rapid colonization of the bivalve larvaeby these pathogens, leading to high larval mortality rates and theloss of production batches (4). The Orientalis clade has a relevantsignificance for bivalve aquaculture since it includes some of themost well-known larval pathogens, such as Vibrio tubiashii subsp.tubiashii,V. tubiashii subsp. europaeus, and the recently describedV. bivalvicida, whose broad range of action was reported in larvaeof different bivalve species (5).V. bivalvicida 605T ( CECT 8855T CAIM 1904T) was orig-inally isolated from an episode of larval mortality of carpet shellclam (Ruditapes decussatus) in a bivalve hatchery located inGalicia(northwest Spain). Genomic DNA was sequenced using an Illu-mina MiSeq sequencer by Sistemas Genómicos (Valencia, Spain)with 100 coverage. Reads were trimmed for quality, ambiguousnucleotides, and adapters and were assembled using SPAdes ver-sion 3.6 (6). QUAST (7) was used to evaluate the assembly. Theassembly produced 91 contigs totaling 4,922,047 bp with an aver-ageGC content of 43.6%. TheN50 contig size is 191,755 bp, withthe largest contig being 691,504 bp. The resulting draft genomesequence was annotated with the Rapid Annotations using Sub-systems Technology (RAST) server, resulting in 4,619 open read-ing frames (8).The genome of V. bivalvicida 605T encodes three putative ex-tracellular proteins that have been characterized in other Vibriospp.: a phospholipase/hemolysin that shows similarity to Plp inV. anguillarum M93Sm (9), a hemolysin annotated as HlyA thatshows similarity to Vah1 in V. anguillarum M93Sm (9), and ametalloprotease that shows similarity to VtpA in V. coralliilyticusRE22 (10). Additional putative extracellular virulence factorsidentified by RAST are five hemolysins and two phospholipases.Two secretion systems (type III and type VI) used to deliver effec-tors directly into a host cell were identified on the V. bivalvicida605T genome. The only conserved domain annotated in the typeIII–injected virulence protein is the YopH N-terminal domain(11). This domain is needed for translocation from the bacteriuminto the eukaryotic host cell.This work constituted the first draft genome description of thenovel larval pathogen of bivalvesV. bivalvicida 605T. This genomeinformation contributes to the study of virulence factors, the de-velopment of new accurate diagnostic methods, and the knowl-edge of the bivalve pathogenic Vibrio spp.Nucleotide sequence accessionnumbers.Thiswhole-genomeshotgun project has been deposited inDDBJ/EMBL/GenBank un-der the accession number LLEI00000000. The version described inthis paper is the second version, LLEI02000000.ACKNOWLEDGMENTSThis study was supported by grants AGL2014–59655 and AGL2013-42628-R from the Ministry of Economy and Competitiveness of Spain.FUNDING INFORMATIONThis work, including the efforts of Juan L. Barja, was funded byMinisteriode Economía y Competitividad (MINECO) (AGL2014-59655). Thiswork, including the efforts of Jesús L. Romalde, was funded byMinisteriode Economía y Competitividad (MINECO) (AGL2013-42628-R).REFERENCES1. Sawabe T, Ogura Y, Matsumura Y, Feng G, Amin AR, Mino S, Naka-gawa S, Sawabe T, Kumar R, Fukui Y, Satomi M, Matsushima R,Thompson FL, Gomez-Gil B, Christen R, Maruyama F, Kurokawa K,Hayashi T. 2013. Updating the Vibrio clades defined by multilocus se-quence phylogeny: proposal of eight new clades, and the description ofVibrio tritonius sp. nov. FrontMicrobiol 4:414. http://dx.doi.org/10.3389/fmicb.2013.00414.2. Al-saari N, Gao F, Rohul AAKM, Sato K, Sato K, Mino S, Suda W,Oshima K, Hattori M, Ohkuma M, Meirelles PM, Thompson FL,Thompson C, Filho GM, Gomez-Gil B, Sawabe T, Sawabe T. 2015.Advanced microbial taxonomy combined with genome-based-crossmarkGenome AnnouncementsMarch/April 2016 Volume 4 Issue 2 e00216-16 genomea.asm.org 1 on August 28, 2017 by UNIV OF RHODE ISLANDhttp://genomea.asm.org/Downloaded from approaches reveals that Vibrio astriarenae sp. nov., an agarolytic marinebacterium, forms a new clade in Vibrionaceae. PLoS One 10:e0136279.http://dx.doi.org/10.1371/journal.pone.0136279.3. Romalde JL, Dieguez AL, Lasa A, Balboa S. 2014. New Vibrio speciesassociated to molluscan microbiota: a review. Front Microbiol 4:413.http://dx.doi.org/10.3389/fmicb.2013.00413.4. Dubert J, Nelson DR, Spinard EJ, Kessner L, Gomez-Chiarri M, daCosta Fd, Prado S, Barja JL. 2016. Following the infection process ofvibriosis in Manila clam (Ruditapes philippinarum) larvae through GFP-tagged pathogenic Vibrio species. J Invertebr Pathol 133:27–33. http://dx.doi.org/10.1016/j.jip.2015.11.008.5. Dubert J, Romalde JL, Prado S, Barja JL. 2016.Vibrio bivalvicida sp. nov.,a novel larval pathogen for bivalvemolluscs reared in a hatchery. Syst ApplMicrobiol 39:8–13. http://dx.doi.org/10.1016/j.syapm.2015.10.006.6. Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapi-dus A, Prjibelsky A, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R,McLean J, Lasken R, Clingenpeel SR, Woyke T, Tesler G, AlekseyevMA, Pevzner PA. 2013. Assembling genomes and mini-metagenomesfromhighly chimeric reads, p. 158–170. InDengM, Jiang R, Sun F, ZhangX (ed), Research in computational molecular biology. Springer, Berlin.http://dx.doi.org/10.1007/978-3-642-37195-0_13.7. Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: qualityassessment tool for genome assemblies. Bioinformatics 29:1072–1075.http://dx.doi.org/10.1093/bioinformatics/btt086.8. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA,Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, OlsonR, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T,Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V,Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations usingSubsystems Technology. BMCGenomics 9:75. http://dx.doi.org/10.1186/1471-2164-9-75.9. Rock JL, Nelson DR. 2006. Identification and characterization of a he-molysin gene cluster in Vibrio anguillarum. Infect Immun 74:2777–2786.http://dx.doi.org/10.1128/IAI.74.5.2777-2786.2006.10. Hasegawa H, Häse CC. 2009. The extracellular metalloprotease of Vibriotubiashii directly inhibits its extracellular haemolysin. Microbiology 155:2296–2305. http://dx.doi.org/10.1099/mic.0.028605-0.11. Evdokimov AG, Tropea JE, Routzahn KM, Copeland TD, Waugh DS.2001. Structure of the N-terminal domain of Yersinia pestis YopH at 2.0-Aresolution. Acta Crystallogr D Biol Crystallogr 57:793–799. http://dx.doi.org/10.1107/S0907444901004875.Dubert et al.Genome Announcements2 genomea.asm.org March/April 2016 Volume 4 Issue 2 e00216-16 on August 28, 2017 by UNIV OF RHODE ISLANDhttp://genomea.asm.org/Downloaded from 

Draft Genome Sequence of the New Pathogen for Bivalve Larvae \u3cem\u3eVibrio bivalvicida\u3c/em\u3e

ABSTRACT
          
            Vibrio bivalvicida
            is a novel pathogen of bivalve larvae responsible for recent vibriosis outbreaks affecting shellfish hatcheries. Here, we announce the draft genome sequence of
            V. bivalvicida
            605
            T
            and describe potential virulence factors.
          </jats:p

Javier Dubert

Edward J. Spinard

David R. Nelson

Marta Gomez-Chiarri

Jesús L. Romalde

Juan L. Barja

Crossref

Genome Announcements

Draft Genome Sequence of the New Pathogen for Bivalve Larvae
            <i>Vibrio bivalvicida</i>

https://digitalcommons.uri.edu/cgi/viewcontent.cgi?article=1033&amp;context=cmb_facpubs

Draft Genome Sequence of the New Pathogen for Bivalve Larvae \u3cem\u3eVibrio bivalvicida\u3c/em\u3e

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